Abstract Background Previous research has revealed the logical mapping of fascicles in both human somatic and pig vagus nerves, but the organization of fascicles within the human vagus nerve remains largely unknown. Understanding its fascicular arrangement would significantly advance our knowledge of the autonomic nervous system and facilitate studies and application of selective vagus nerve stimulation to avoid off-target effects. The purpose of this study was to trace the thoracic branches of human vagus nerves, investigate their fascicular organization, and analyze the nerves histologically and morphologically. Methods Both left and right vagus nerves were dissected from human cadavers, preserving the cardiac, recurrent laryngeal, and pulmonary branches. The nerves were prepared, scanned using microCT, and the fascicles segmented and traced from their branching points. Histology and immunohistochemistry were performed for morphological analysis and validation of the microCT segmentation. The data was then analyzed and compared between nerves. Results The organization of the cardiac, pulmonary, and recurrent laryngeal fascicles was observed for a short distance from their entry point into the nerves. Initially, left vagus nerves showed merging of cardiac and pulmonary fascicles, while the recurrent laryngeal fascicles remained separate. In right vagus nerves, the cardiac fascicles merged with both pulmonary and recurrent laryngeal fascicles. MicroCT imaging limitations prevented visualization and tracing of fiber organization within merged fascicles. Immunohistochemistry and morphological analysis revealed that right vagus nerves were larger and had more fascicles than the left and fascicle counts varied along the nerve, indicating anastomoses. The superior cardiac branch was separate from other fascicles near the VNS cuff placement. Conclusions It is possible that organ-specific fibers may still retain some spatial organization despite most fascicles being merged at cervical level. However, fiber tracing and in vivo studies could provide valuable information beyond microCT to resolve this further. The separate superior cardiac fascicles offer potential for targeted neuromodulation of the heart, benefiting conditions like myocardial infarction, heart failure, and atrial fibrillation. Overall, the study provides insights into the morphology and anatomy of human vagus nerves. Our findings thereby contribute to the development of selective vagus nerve stimulation strategies for more precise autonomic regulation.